omdLast

#!@Python3_EXECUTABLE@
"""OpenMD File Extractor
 
Makes omd file from the last good frame of OpenMD dump file.
 
Usage: omdLast
 
Options:
  -h, --help              show this help
  -m, --meta-data=...     use specified OpenMD (.dump) file
 
Example:
   omdLast -m Ar.dump
 
"""
 
__author__ = "Hemanta Bhattarai (hbhattar@nd.edu), Charles Vardeman (cvardema@nd.edu)"
__copyright__ = "Copyright (c) 2004-present The University of Notre Dame. All Rights Reserved."
__license__ = "OpenMD"
 
import sys
import getopt
import string
import os
 
 
_haveMDFileName = 0
 
 
def usage():
    print(__doc__)
 
 
def getLastFrame(mdFileName):
    mdFile = open(mdFileName, 'r')
 
    (filepath, filename) = os.path.split(mdFileName)
 
    (outfilePrefix, ext)  = os.path.splitext(filename)
 
 
 
    metaDataFrame = []
    haveMetaData = 0
    haveMetaDataEnd = 0
# Find OpenMD version info first
    line = mdFile.readline()
    while True:
        if '<OOPSE version=' in line or '<OpenMD version=' in line:
            OpenMDversion = line
            break
        line = mdFile.readline()
 
# Rewind file and find start of MetaData block
 
    mdFile.seek(0)
    breakLoop = False
    line = mdFile.readline()
 
    while True:
        if '<MetaData>' in line:
            while 2:
                metaDataFrame.append(line)
                line = mdFile.readline()
                if '</MetaData>' in line:
                    metaDataFrame.append(line)
                    breakLoop = True
                    break
        if breakLoop:
            break
        line = mdFile.readline()
 
 
 
 
    # reading last valid frame from dump file
    mdFile.seek(0)
    framePos = 0
    foundFrames = 0;
    lineReversed = reversed(mdFile.readlines())
    SnapshotFrameReversed = []
    writeSnapshotFrameReversed = False
    for line in lineReversed:
        splittedLine = line.split()
        if '</Snapshot>' in splittedLine or writeSnapshotFrameReversed == True:
            writeSnapshotFrameReversed = True
            SnapshotFrameReversed.append(line)
 
        if '<Snapshot>' in splittedLine and writeSnapshotFrameReversed:
            break
 
    mdFile.close()
 
    # checking if there exist valid frame
    try:
        SnapshotFrameReversed[0]
    except IndexError:
        print("\t\tError: %s doesn't have any valid frames." %filename)
        return None
 
    # writing out the valid frame
 
    outfilename = outfilePrefix + "_lastframe" + ".omd"
    outFile = open(outfilename, 'w')
    outFile.write(OpenMDversion)
    for metaline in metaDataFrame:
        outFile.write(metaline)
 
    for lineNumber in range(1,len(SnapshotFrameReversed)+1):
        outFile.write(SnapshotFrameReversed[-lineNumber])
 
    outFile.write("</OpenMD>")
    outFile.close()
 
 
 
 
def main(argv):
    try:
        opts, args = getopt.getopt(argv, "hm:", ["help", "meta-data=", ""])
    except getopt.GetoptError:
        usage()
        sys.exit(2)
    for opt, arg in opts:
        if opt in ("-h", "--help"):
            usage()
            sys.exit()
        elif opt in ("-m", "--meta-data"):
            mdFileName = arg
            global _haveMDFileName
            _haveMDFileName = 1
 
 
 
    if (_haveMDFileName != 1):
        usage()
        print("No OpenMD file was specified")
        sys.exit()
 
    getLastFrame(mdFileName)
 
 
if __name__ == "__main__":
    if len(sys.argv) == 1:
        usage()
        sys.exit()
    main(sys.argv[1:])